Fig. 8

Summary of somatic SVs detected in PacBio long-read sequencing data and assembled contigs. A Counts of somatic SVs with supports from two or more calling methods in tumor sample (HCC1395) using PacBio long reads and assembled contigs on HCC1395BL_v1.0 as compared to GRCh38 references. B Mapping 744 GRCh38-based somatic SVs that were supported by three or more calling methods onto HCC1395BL_v1.0, 531 SVs were mapped with matched SVs on HCC1395BL_v1.0, and 129 SVs were mapped but without matching SVs, whereas 84 SVs were considered “unmapped” on HCC1395BL_v1.0. C KEGG pathway enrichment analysis for 86 genes overlapped with 91 novel SVs. Shown here are the top 10 enriched pathways with “odds ratio” (zScore) and log (p-value) on the y-axis. The numeric labels are the enriched gene counts versus the total genes in each pathway. D Repeat annotation for the sequences of 72 deletions from 91 SVs that overlapped 86 gene regions using RepeatMasker showed that 32 deletions overlapped 10 classes of repeat families, among them 17 SINE/Alu, 8 simple repeats, and 3 retroposon/SVA